query on a pre-process step involving GFF3

Question

[prasundutta87]

Hello,

So, I had to update the chromosome names in a GFF3 file. For ease, I removed the lines that started with #. This helped me to get a clean tab separated GFF3 file that I could use in my R script for updating the chromosome names. The reason I removed the lines because some lines had something like this:

##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=89462
##sequence-region NW_020229131.1 1 29085

I am aware that lines that start with ## are directives and can be ignored by parsers. So, by removing them, I technically did not de-format the GFF3 format.

If there are some loopholes or if I did anything, kindly correct me.

[Sej Modha]

Removing comments should not be a problem but updating names of the chromosome would have an impact on other things, e.g. if you have a corresponding genome .fasta file then you should update the sequence headers in that file too.

[prasundutta87]

Thanks, Sej..I have the other way round issue..I updated my GFF3 file chromosome names to match my reference genome..